Freshwater, brackish and marine metagenomes from coastal lagoons and reservoirs and the South Atlantic Microbial Observatory (SAMO) in Uruguay

This study describes the microbial communities of four different coastal lagoons (Laguna de Rocha, Laguna de Castillos, Laguna de Briozzo, Laguna Negra), a reservoir (Represa de India Muerta) and a sample from the South Atlantic Microbial Observatory (SAMO) in Uruguay using high throughput metagenomic sequencing with long- and short read technologies (Oxford Nanopore and Illumina). Water samples were taken from the surface or mid-water column (2 m depth for Laguna de Briozzo, 0.5 m for the other sites), at a single site or - in case of Lagoons with a salinity gradient, i.e., Laguna de Rocha, Laguna de Castillos – from 2-3 different sites with brackish and freshwater conditions, respectively. 0.1-9 L of water were prefiltered through a plankton net (20 µm) and a 5-µm filter and then filtered onto polysulfone filters with a pore size of 0.22 µm until filters were clogged. DNA was extracted from the 0.22 µm filter (small, planktonic fraction) to obtain genomic DNA of the microbial community.